The slowscale stochastic simulation algorithm
Abstract
Reactions in real chemical systems often take place on vastly different time scales, with "fast" reaction channels firing very much more frequently than "slow" ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will necessarily spend most of its time simulating the more numerous fast reaction events. This is a frustratingly inefficient allocation of computational effort when dynamical stiffness is present, since in that case a fast reaction event will be of much less importance to the system's evolution than will a slow reaction event. For such situations, this paper develops a systematic approximate theory that allows one to stochastically advance the system in time by simulating the firings of only the slow reaction events. Developing an effective strategy to implement this theory poses some challenges, but as is illustrated here for two simple systems, when those challenges can be overcome, very substantial increases in simulation speed can be realized.
 Publication:

Journal of Chemical Physics
 Pub Date:
 January 2005
 DOI:
 10.1063/1.1824902
 Bibcode:
 2005JChPh.122a4116C
 Keywords:

 82.40.g;
 05.40.a;
 87.10.+e;
 Chemical kinetics and reactions: special regimes and techniques;
 Fluctuation phenomena random processes noise and Brownian motion;
 General theory and mathematical aspects